rs35825847

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001220500.2(FCER2):​c.761G>A​(p.Ser254Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000643 in 1,602,300 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 2 hom. )

Consequence

FCER2
NM_001220500.2 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37
Variant links:
Genes affected
FCER2 (HGNC:3612): (Fc epsilon receptor II) The protein encoded by this gene is a B-cell specific antigen, and a low-affinity receptor for IgE. It has essential roles in B cell growth and differentiation, and the regulation of IgE production. This protein also exists as a soluble secreted form, then functioning as a potent mitogenic growth factor. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jul 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.022611588).
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FCER2NM_001220500.2 linkuse as main transcriptc.761G>A p.Ser254Asn missense_variant 11/11 ENST00000597921.6
FCER2NM_002002.5 linkuse as main transcriptc.761G>A p.Ser254Asn missense_variant 11/11
FCER2NM_001207019.3 linkuse as main transcriptc.758G>A p.Ser253Asn missense_variant 10/10
FCER2XM_005272462.5 linkuse as main transcriptc.761G>A p.Ser254Asn missense_variant 11/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FCER2ENST00000597921.6 linkuse as main transcriptc.761G>A p.Ser254Asn missense_variant 11/111 NM_001220500.2 P2

Frequencies

GnomAD3 genomes
AF:
0.000342
AC:
52
AN:
152196
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00125
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000530
AC:
12
AN:
226540
Hom.:
0
AF XY:
0.0000402
AC XY:
5
AN XY:
124394
show subpopulations
Gnomad AFR exome
AF:
0.000692
Gnomad AMR exome
AF:
0.0000918
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000359
AC:
52
AN:
1449986
Hom.:
2
Cov.:
31
AF XY:
0.0000222
AC XY:
16
AN XY:
720076
show subpopulations
Gnomad4 AFR exome
AF:
0.00135
Gnomad4 AMR exome
AF:
0.0000921
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000502
GnomAD4 genome
AF:
0.000335
AC:
51
AN:
152314
Hom.:
0
Cov.:
32
AF XY:
0.000443
AC XY:
33
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.00123
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000641
Hom.:
0
Bravo
AF:
0.000310
ESP6500AA
AF:
0.000461
AC:
2
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000582
AC:
7

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.081
BayesDel_addAF
Benign
-0.73
T
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.43
DANN
Benign
0.22
DEOGEN2
Benign
0.016
.;T;T
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.022
N
LIST_S2
Benign
0.39
T;.;T
M_CAP
Benign
0.0028
T
MetaRNN
Benign
0.023
T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
-0.56
.;N;N
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-0.030
N;N;.
REVEL
Benign
0.012
Sift
Benign
0.15
T;T;.
Sift4G
Benign
0.10
T;T;T
Polyphen
0.0
.;B;B
Vest4
0.056
MVP
0.22
MPC
0.066
ClinPred
0.0057
T
GERP RS
-2.8
Varity_R
0.23
gMVP
0.21

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35825847; hg19: chr19-7754284; API